I like Larry's idea best, but here's another one for consideration:

1) Drill small (say, 1/4" dia) holes where the pad-eyes will be. 2) Poke a string through each one and down to the cockpit opening. 3) Attach a small cap (like from the cover of a spring water bottle) to each one and pull tight. This will bring the cap under your pad-eye hole. 4) Keeping string taught, fill with thickened epoxy. 5) When cured, pre-drill a small hole only partway through the epoxy plug. 6) Put a dab of epoxy in the holes and install pad-eyes with wood screws that match the machine screws you've used on the others.

Similarily, you could probably just put extra pieces of plywood down there, glued with thickened epoxy, working with a long stick.

Dean